Search

Forest tree species are highly vulnerable to the effects of climate change. As sessile organisms with long generation times, their adaptation to a local changing environment may rely on epigenetic modifications when allele frequencies are not able to shift fast enough. However, the current lack of knowledge on this field is remarkable, due to many challenges that researchers face when studying this issue. Huge genome sizes, absence of reference genomes and annotation, and having to analyze huge amounts of data are among these difficulties, which limit the current ability to understand how climate change drives tree species epigenetic modifications. In spite of this challenging framework, some insights on the relationships among climate change-induced stress and epigenomics are coming. Advances in DNA sequencing technologies and an increasing number of studies dealing with this topic must boost our knowledge on tree adaptive capacity to changing environmental conditions. Here, we discuss challenges and perspectives in the epigenetics of climate change-induced forests decline, aiming to provide a general overview of the state of the art., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 García-García, Méndez-Cea, Martín-Gálvez, Seco, Gallego and Linares.)

Bacterial communities within avian nests are considered an important determinant of egg viability, potentially selecting for traits that confer embryos with protection against trans-shell infection. A high bacterial density on the eggshell increases hatching failure, whether this effect could be due to changes in bacterial community or just a general increase in bacterial density. We explored this idea using intra- and interspecific comparisons of the relationship between hatching success and eggshell bacteria characterized by culture and molecular techniques (fingerprinting and high-throughput sequencing). We collected information for 152 nests belonging to 17 bird species. Hatching failures occurred more frequently in nests with higher density of aerobic mesophilic bacteria on their eggshells. Bacterial community was also related to hatching success, but only when minority bacterial operational taxonomic units were considered. These findings support the hypothesis that bacterial density is a selective agent of embryo viability, and hence a proxy of hatching failure only within species. Although different avian species hold different bacterial densities or assemblages on their eggs, the association between bacteria and hatching success was similar for different species. This result suggests that interspecific differences in antibacterial defenses are responsible for keeping the hatching success at similar levels in different species.

Background: The genomes of laboratory rat strains are characterised by a mosaic haplotype structure caused by their unique breeding history. These mosaic haplotypes have been recently mapped by extensive sequencing of key strains. Comparison of genomic variation between two closely related rat strains with different phenotypes has been proposed as an effective strategy for the discovery of candidate strain-specific regions involved in phenotypic differences. We developed a method to prioritise strain-specific haplotypes by integrating genomic variation and genomic regulatory data predicted to be involved in specific phenotypes. Specifically, we aimed to identify genomic regions associated with Metabolic Syndrome (MetS), a disorder of energy utilization and storage affecting several organ systems., Results: We compared two Lyon rat strains, Lyon Hypertensive (LH) which is susceptible to MetS, and Lyon Low pressure (LL), which is susceptible to obesity as an intermediate MetS phenotype, with a third strain (Lyon Normotensive, LN) that is resistant to both MetS and obesity. Applying a novel metric, we ranked the identified strain-specific haplotypes using evolutionary conservation of the occupancy three liver-specific transcription factors (HNF4A, CEBPA, and FOXA1) in five rodents including rat. Consideration of regulatory information effectively identified regions with liver-associated genes and rat orthologues of human GWAS variants related to obesity and metabolic traits. We attempted to find possible causative variants and compared them with the candidate genes proposed by previous studies. In strain-specific regions with conserved regulation, we found a significant enrichment for published evidence to obesity-one of the metabolic symptoms shown by the Lyon strains-amongst the genes assigned to promoters with strain-specific variation., Conclusions: Our results show that the use of functional regulatory conservation is a potentially effective approach to select strain-specific genomic regions associated with phenotypic differences among Lyon rats and could be extended to other systems.

Selective pressures imposed by pathogenic microorganisms to embryos have selected in hosts for a battery of antimicrobial lines of defenses that includes physical and chemical barriers. Due to the antimicrobial properties of volatile compounds of green plants and of chemicals of feather degrading bacteria, the use of aromatic plants and feathers for nest building has been suggested as one of these barriers. However, experimental evidence suggesting such effects is scarce in the literature. During two consecutive years, we explored experimentally the effects of these nest materials on loads of different groups of bacteria (mesophilic bacteria, Enterobacteriaceae, Staphylococcus and Enterococcus) of eggshells in nests of spotless starlings (Sturnus unicolor) at the beginning and at the end of the incubation period. This was also explored in artificial nests without incubation activity. We also experimentally increased bacterial density of eggs in natural and artificial nests and explored the effects of nest lining treatments on eggshell bacterial load. Support for the hypothetical antimicrobial function of nest materials was mainly detected for the year and location with larger average values of eggshell bacterial density. The beneficial effects of feathers and plants were more easily detected in artificial nests with no incubation activity, suggesting an active role of incubation against bacterial colonization of eggshells. Pigmented and unpigmented feathers reduced eggshell bacterial load in starling nests and artificial nest boxes. Results from artificial nests allowed us to discuss and discard alternative scenarios explaining the detected association, particularly those related to the possible sexual role of feathers and aromatic plants in starling nests. All these results considered together confirm the antimicrobial functionality mainly of feathers but also of plants used as nest materials, and highlight the importance of temporally and geographically environmental variation associated with risk of bacterial proliferation determining the strength of such effects. Because of costs associated to nest building, birds should adjust nest building effort to expected bacterial environments during incubation, a prediction that should be further explored.

Parent-offspring conflict theory predicts that begging behaviour could escalate continuously over evolutionary time if it is not prevented by costliness of begging displays. Three main potential physiological costs have been proposed: growth, immunological and metabolic costs. However, empirical evidence on this subject remains elusive because published results are often contradictory. In this study, we test for the existence of these three potential physiological costs of begging in house sparrow (Passer domesticus) nestlings by stimulating a group of nestlings to beg for longer and another group for shorter periods than in natural conditions. All nestlings were fed with the same quantity of food. Our study involves a long-term experimental treatment for begging studies (five consecutive days). Long-term studies frequently provide clearer results than short-term studies and, sometimes, relevant information not reported by the latter ones. Our long-term experiment shows (i) a clear effect on the immune response even since the first measurement (6 hours), but it was higher during the second (long-term) than during the first (short-term) test; (ii) evidence of a growth cost of begging in house sparrow nestlings not previously found by other studies; (iii) body condition was affected by our experimental manipulation only after 48 hour; (iv) a metabolic cost of begging never previously shown in any species, and (v) for the first time, it has shown a simultaneous effect of the three potential physiological costs of begging: immunocompetence, growth, and metabolism. This implies first, that a multilevel trade-off can occur between begging and all physiological costs and, second, that a lack of support in a short-term experiment for the existence of a tested cost of begging does not mean absence of that cost, because it can be found in a long-term experiment.

One of the best-known outcomes of coevolution between species is the rejection of mimetic parasite eggs by avian hosts, which has evolved to reduce costly cuckoo parasitism. How this behavioral adaptation varies along the life of individual hosts remains poorly understood. Here, we identify for the first time, lifetime patterns of egg rejection in a parasitized long-lived bird, the magpie Pica pica and show that, during the years they were studied, some females accept, others reject, and some others modify their response to model eggs, in all cases switching from acceptance to rejection. Females tested in their first breeding attempt always accepted the model egg, even those individuals whose mothers were egg rejecters. A longitudinal analysis showed that the probability of egg rejection increased with the relative age of the female, but was not related to the risk of parasitism in the population. We conclude that ontogeny plays a fundamental role in the process leading to egg rejection in magpies., (© 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.)

Reproductive success of brood parasites largely depends on appropriate host selection and, although the use of inadvertent social information emitted by hosts may be of selective advantage for cuckoos, this possibility has rarely been experimentally tested. Here, we manipulated nest size and clutch colouration of magpies (Pica pica), the main host of great spotted cuckoos (Clamator glandarius). These phenotypic traits may potentially reveal information about magpie territory and/or parental quality and could hence influence the cuckoo's choice of host nests. Experimentally reduced magpie nests suffered higher predation rate, and prevalence of cuckoo parasitism was higher in magpie nests with the densest roofs, which suggests a direct advantage for great spotted cuckoos choosing this type of magpie nest. Colouration of magpie clutches was manipulated by adding one artificial egg (blue or cream colouration) at the beginning of the egg-laying period. We found that host nests holding an experimental cream egg experienced a higher prevalence of cuckoo parasitism than those holding a blue-coloured egg. Results from these two experiments suggest that great spotted cuckoos cue on magpie nest characteristics and the appearance of eggs to decide parasitism, and confirm, for the first time, the ability of cuckoos to distinguish between eggs of different colours within the nest of their hosts. Several hypothetical scenarios explaining these results are discussed.

Climatic conditions, through their effects on resource availability, may affect important life history strategies and trade-offs in animals, as well as their interactions with other organisms such as parasites. This impact may depend on species-specific pathways of development that differ even among species with similar resource requirements (e.g., avian brood parasites and their hosts). Here we explore the degree of covariation between environmental-climatic conditions and nestling phenotypes (i.e., tarsus length, body mass, immune response to phytohemagglutinin injection) and ectoparasite loads of great spotted cuckoos (Clamator glandarius) and those of their magpie (Pica pica) hosts, both within and among 11 study years (1997-2011). Our main results were that (1) nestling phenotypes differed among years, but differently for great spotted cuckoos and magpies; (2) nestling phenotypes showed significant among-year covariation with breeding climatic conditions (temperature and precipitation); and (3) these associations differed for cuckoos and magpies for some phenotypic traits. As the average temperature at the beginning of the breeding season (April) increased, body mass and tarsus length increased only for cuckoos, but not for magpie hosts, while immune response decreased in both species. Finally, (4) the strength of the within-year relationships between the probability of ectoparasitism by Carnus hemapterus flies and laying date (used as an estimate of the within-year variation in climatic conditions) was negatively affected by the annual accumulated precipitation in April. These results strongly suggest that variation in climatic conditions would result in asymmetric effects on different species with respect to the probability of ectoparasitism, immunity and body size. Such asymmetric effects may affect animal interactions in general and those of brood parasites and their hosts in particular.

Environmental characteristics of neighboring locations are generally more similar than those of distant locations. Selection pressures due to parasitism and other environmental conditions shape life history traits of hosts; thus, the probability of parasitism should be associated with the strength of spatial autocorrelation in life history and defensive traits of their hosts. Here we test this hypothesis in three different subpopulations of Magpie (Pica pica) parasitized by the Great Spotted Cuckoo (Clamator glandarius) during three breeding seasons. In some of the years and study plots, we found evidence of positive spatial autocorrelations for clutch size and parasitism rate, but not for laying date. As predicted, brood parasitism was associated with the strength of these spatial autocorrelations. Magpies that bred close to each other in areas of high risk of parasitism responded similarly to experimental parasitic eggs. Moreover, an elevated risk of parasitism eliminated the spatial autocorrelation for clutch size, which became randomly distributed. We discuss possible mechanisms explaining these associations, which may have important consequences for estimating evolutionary responses of hosts to parasitic infections and, therefore, for epidemiological, ecological, and evolutionary studies of host-parasite relationships.

Background: Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hybrids, clones and ploidy. Microsatellites also have the highest cross-species utility of all types of markers used for genotyping, but, despite this, when isolated from a single species, only a relatively small proportion will be of utility. Marker development of any type requires skill and time. The availability of sufficient "off-the-shelf" markers that are suitable for genotyping a wide range of species would not only save resources but also uniquely enable new comparisons of diversity among taxa at the same set of loci. No other marker types are capable of enabling this. We therefore developed a set of avian microsatellite markers with enhanced cross-species utility., Results: We selected highly-conserved sequences with a high number of repeat units in both of two genetically distant species. Twenty-four primer sets were designed from homologous sequences that possessed at least eight repeat units in both the zebra finch (Taeniopygia guttata) and chicken (Gallus gallus). Each primer sequence was a complete match to zebra finch and, after accounting for degenerate bases, at least 86% similar to chicken. We assessed primer-set utility by genotyping individuals belonging to eight passerine and four non-passerine species. The majority of the new Conserved Avian Microsatellite (CAM) markers amplified in all 12 species tested (on average, 94% in passerines and 95% in non-passerines). This new marker set is of especially high utility in passerines, with a mean 68% of loci polymorphic per species, compared with 42% in non-passerine species., Conclusions: When combined with previously described conserved loci, this new set of conserved markers will not only reduce the necessity and expense of microsatellite isolation for a wide range of genetic studies, including avian parentage and population analyses, but will also now enable comparisons of genetic diversity among different species (and populations) at the same set of loci, with no or reduced bias. Finally, the approach used here can be applied to other taxa in which appropriate genome sequences are available.

Brood parasites usually reduce their host's breeding success, resulting in strong selection for the evolution of host defences. Intriguingly, some host individuals/populations show no defence against parasitism, which has been explained within the frame of three different evolutionary hypotheses. One of these hypotheses posits that intermediate levels of defence at the population level may result from nonrandom distribution of parasitism among host individuals (i.e. structured parasitism). Empirical evidence for structured brood parasitism is, however, lacking for hosts of European cuckoos due to the absence of long-term studies. Here, we seek to identify the patterns of structured parasitism by studying great spotted cuckoo parasitism on individual magpie hosts over five breeding seasons. We also aim to identify whether individual characteristics of female magpies and/or their territories were related to the status of repeated parasitism. We found that 28·3% of the females in our population consistently escaped from cuckoo parasitism. Only 11·3% of females were always parasitized, and the remaining 60·4% changed their parasitism status. The percentage of females that maintained their status of parasitism (i.e. either parasitized or nonparasitized) between consecutive years varied over the study. Females that never suffered cuckoo parasitism built bigger nests than parasitized females at the beginning of the breeding season and smaller nests than those of parasitized females later in the season. Nonparasitized females also moved little from year to year and preferred areas with different characteristics over the course of the breeding season than parasitized females. Overall, females escaping from cuckoo parasitism reared twice as many chicks per year than those that were parasitized. In conclusion, our study reveals for first time the existence of a structured pattern of cuckoo parasitism based on phenotypic characteristics of individual hosts and of their territories., (© 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.)

There is increasing interest in noninvasive DNA sampling techniques. In birds, there are several methods proposed for sampling DNA, and of these, the use of eggshell swabbing is potentially applicable to a wide range of species. We estimated the effectiveness of this method in the wild by sampling the eggs of 23 bird species. Sampling of eggs was performed twice per nest, soon after the clutch was laid and again at the end of egg incubation. We genotyped DNA samples using a set of five conserved microsatellite markers, which included a Z-linked locus and a sex-typing marker. We successfully collected avian DNA from the eggs of all species tested and from 88.48% of the samples. In most of the cases, the DNA concentration was low (ca. 10 ng/μL). The number of microsatellite loci amplified per sample (0-5) was used as a measure of the genotyping success of the sample. On average, we genotyped 3.01 ± 0.12 loci per sample (mean ± SE), and time of sampling did not seem to have an effect; however, genotyping success differed among species and was greater in those species that used feather material for lining their nest cups. We also checked for the occurrence of possible genotyping errors derived from using samples with very low DNA quantities (i.e. allelic dropout or false alleles) and for DNA contamination from individuals other than the mother, which appeared at a moderate rate (in 44% of the PCR replicates and in 17.36% of samples, respectively). Additionally, we investigated whether the DNA on eggshells corresponded to maternal DNA by comparing the genotypes obtained from the eggshells to those obtained from blood samples of all the nestlings for six nests of magpies. In five of the six magpie nests, we found evidence that the swab genotypes were a mixture of genotypes from both parents and this finding was independent of the time of incubation. Thus, our results broadly confirm that the swabbing of eggshells can be used as a noninvasive method for obtaining DNA and is applicable across a wide range of bird species. Nonetheless, genotyping errors should be properly estimated for each species by using a suite of highly polymorphic loci. These errors may be resolved by sampling only recently laid eggs (to avoid non-maternal DNA contamination) or by performing several PCR replicates per sample (to avoid allelic dropout and false alleles) and/or by increasing the amount of DNA used in the PCR through increasing the volume of the PCR or increasing the concentration of template DNA., (© 2010 Blackwell Publishing Ltd.)

Several experimental results support the existence of costs associated with exaggerated begging behaviour, which are assumed by some theoretical models of honest signalling in parent-offspring communication. However, to understand how honest begging behaviour is evolutionarily maintained in nature, the long-term cost-benefit output associated with exaggerated signals should also be estimated. As far as we know, the net cost-benefit balance of begging display has not previously been explored. Here, we used an appetite stimulant, cyproheptadine hydrochloride, to increase the feeling of hunger in some magpie nestlings. Supporting the use of cyproheptadine to manipulate hunger level and thereby begging behaviour, we found that experimental nestlings increased the frequency of begging and received more food than their control nestmates. Contrary to the expectation that physiological costs per se counteract the associated benefits of escalated begging signals, we found that near-fledging experimental magpies showed a better physical condition than control nestlings. These findings stress the interesting question of why magpie nestlings do not show to adults an escalated level of hunger if it implies an advantage. We discuss the responsibility of inclusive fitness costs and indirect genetic effects for the maintenance of honesty in parent-offspring communication.

It remains largely unknown which factors affect the innate immune responses of free-living birds. Nevertheless, the degree of innate immunity may play a crucial role in an individual's survival as it procures the first defence against pathogens. We manipulated the ectoparasite load of great tit (Parus major) nests by infesting them with hen fleas (Ceratophyllus gallinae) before egg laying. We subsequently quantified natural antibody (NAb) concentration and complement activation in nestlings and adult females during breeding and post-breeding periods. NAb concentrations increased in nestlings and adult females breeding in flea-infested nest boxes during the nestling provisioning period, but not in breeding females during incubation. In contrast, parasite abundance did not affect levels of complement activity in females. NAb levels of nestlings were already fully developed at the end of the nestling stage, but complement activation was only observed post-fledging. Concentrations of NAbs and complement activation of adult females were significantly lower during the breeding season compared with post-breeding levels, but did not differ between incubation and chick rearing. Further experimental studies in species that vary in life-history strategies will allow us to unravel the mechanisms underlying the observed variation in innate immune defences.

We have developed a new approach to create microsatellite primer sets that have high utility across a wide range of species. The success of this method was demonstrated using birds. We selected 35 avian EST microsatellite loci that had a high degree of sequence homology between the zebra finch Taeniopygia guttata and the chicken Gallus gallus and designed primer sets in which the primer bind sites were identical in both species. For 33 conserved primer sets, on average, 100% of loci amplified in each of 17 passerine species and 99% of loci in five non-passerine species. The genotyping of four individuals per species revealed that 24-76% (mean 48%) of loci were polymorphic in the passerines and 18-26% (mean 21%) in the non-passerines. When at least 17 individuals were genotyped per species for four Fringillidae finch species, 71-85% of loci were polymorphic, observed heterozygosity was above 0.50 for most loci and no locus deviated significantly from Hardy-Weinberg proportions. This new set of microsatellite markers is of higher cross-species utility than any set previously designed. The loci described are suitable for a range of applications that require polymorphic avian markers, including paternity and population studies. They will facilitate comparisons of bird genome organization, including genome mapping and studies of recombination, and allow comparisons of genetic variability between species whilst avoiding ascertainment bias. The costs and time to develop new loci can now be avoided for many applications in numerous species. Furthermore, our method can be readily used to develop microsatellite markers of high utility across other taxa., (© 2009 Blackwell Publishing Ltd.)

One-hundred and two unique loci were isolated from a microsatellite-enriched black-billed magpie Pica pica genomic library. Sixteen of these new loci, along with 148 existing microsatellite passerine loci, were tested for polymorphism in four unrelated black-billed magpies. We identified a total of 43 unique polymorphic loci (10 and 33 respectively) that we characterized in 24 unrelated individuals from a population in Guadix, Spain. The putative chromosomal locations of loci polymorphic in black-billed magpie were assigned based on the location of their orthologues in the assembled zebra finch and chicken genomes., (© 2009 Blackwell Publishing Ltd.)

The level of defense against great spotted cuckoo (Clamator glandarius) parasitism in different European populations of magpie (Pica pica) depends on selection pressures due to parasitism and gene flow between populations, which suggests the existence of coevolutionary hot spots within a European metapopulation. A mosaic of coevolution is theoretically possible at small geographical scales and with strong gene flow, because, among other reasons, plots may differ in productivity (i.e., reproductive success of hosts in the absence of parasitism) and defensive genotypes theoretically should be more common in plots of high productivity. Here, we tested this prediction by exploring the relationship between parasitism rate, level of defense against parasitism (estimated as both rejection rate and the frequency of the 457bp microsatellite allele associated with foreign egg rejection in magpies), and some variables related to the productivity (average laying date, clutch size, and number of hatchlings per nest) of magpies breeding in different subpopulations. We found that both estimates of defensive ability (egg rejection rate and frequency of the 457bp allele) covaried significantly with between-plot differences in probability of parasitism, laying date, and number of hatchlings per nest. Moreover, the parasitism rate was larger in more productive plots. These results confirm the existence of a mosaic of coevolution at a very local geographical scale, and the association between laying date and number of hatchlings with variables related to defensive ability and the selection pressure arising from parasitism supports the prediction of coevolutionary gradients in relation to host productivity.